The solution of crystal structures and in-depth structural analysis play a pivotal role in current efforts for rational structure-based vaccine design. However, the structures for many important targets, such as viral surface proteins, haven proven extremely difficult to determine using traditional methods such as protein crystallization and NMR. This presents a significant obstacle to structure-based vaccine design efforts, which rely heavily on the availability of high-quality atomic-level structural information. Computational tools that allow modeling and molecular dynamics simulation of proteins at different levels of structural detail can provide a rational basis for the molecular design of proteins more suitable for crystallization, thus enabling atomic-level characterization of otherwise evasive targets. Moreover, once the structure of a particular target is determined, computational tools can also assist in structural analysis, to help extract biologically meaningful data and to guide new experimental efforts. Here we develop and utilize computational tools to assist in protein crystallization and structural analysis.